[modeller_usage] Modeling antibody

Hi, I am trying to model an antibody variable region using Modeller. I have two questions : 1. I have modelled the heavy chain and Light chain seperately. Now, how can I orient this two chains to generate the complete molecule?

2. CDR loops of antibodies have specific canonical structures, which depends upon loop length, hydrogen bond ladder etc. Can I modify Modeller to build the loops as per the canonical structures?

With regards Biplab -- Biplab Bose, Ph. D Lecturer, Biological Sciences Group, Birla Institute of Technology & Science (BITS), Pilani, Rajasthan, INDIA PIN-333031 Ph.# 9828717874 http://www.biplabbose.wb.st http://www.bits-pilani.ac.inBITS, Pilani